Ziller 2015, Epigenetic footprints during neural differentiation.

Description

Histone modification maps (H3K27ac, H3K27me3, H3K4me1, H3K4me3) in human ES cells undergoing neural differentiation.

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1521740.sga ERG|H3K27ac|rep1 H3K27ac GSM1521740
2 GSM1521745.sga ERG|H3K27ac|rep2 H3K27ac GSM1521745
3 GSM1521741.sga ERG|H3K27me3|rep1 H3K27me3 GSM1521741
4 GSM1521746.sga ERG|H3K27me3|rep2 H3K27me3 GSM1521746
5 GSM1521742.sga ERG|H3K4me1|rep1 H3K4me1 GSM1521742
6 GSM1521747.sga ERG|H3K4me1|rep2 H3K4me1 GSM1521747
7 GSM1521743.sga ERG|H3K4me3|rep1 H3K4me3 GSM1521743
8 GSM1521748.sga ERG|H3K4me3|rep2 H3K4me3 GSM1521748
9 GSM1521744.sga ERG|WCE|rep1 WCE GSM1521744
10 GSM1521749.sga ERG|WCE|rep2 WCE GSM1521749
11 GSM1521721.sga ESC|H3K27ac|rep1 H3K27ac GSM1521721
12 GSM1521726.sga ESC|H3K27ac|rep2 H3K27ac GSM1521726
13 GSM1521722.sga ESC|H3K27me3|rep1 H3K27me3 GSM1521722
14 GSM1521727.sga ESC|H3K27me3|rep2 H3K27me3 GSM1521727
15 GSM1521723.sga ESC|H3K4me1|rep1 H3K4me1 GSM1521723
16 GSM1521728.sga ESC|H3K4me1|rep2 H3K4me1 GSM1521728
17 GSM1521724.sga ESC|H3K4me3|rep1 H3K4me3 GSM1521724
18 GSM1521729.sga ESC|H3K4me3|rep2 H3K4me3 GSM1521729
19 GSM1521725.sga ESC|WCE|rep1 WCE GSM1521725
20 GSM1521750.sga MRG|H3K27ac|rep1 H3K27ac GSM1521750
21 GSM1521755.sga MRG|H3K27ac|rep2 H3K27ac GSM1521755
22 GSM1521751.sga MRG|H3K27me3|rep1 H3K27me3 GSM1521751
23 GSM1521756.sga MRG|H3K27me3|rep2 H3K27me3 GSM1521756
24 GSM1521752.sga MRG|H3K4me1|rep1 H3K4me1 GSM1521752
25 GSM1521757.sga MRG|H3K4me1|rep2 H3K4me1 GSM1521757
26 GSM1521753.sga MRG|H3K4me3|rep1 H3K4me3 GSM1521753
27 GSM1521758.sga MRG|H3K4me3|rep2 H3K4me3 GSM1521758
28 GSM1521761.sga MRG|OTX2|rep1 OTX2 GSM1521761
29 GSM1521754.sga MRG|WCE|rep1 WCE GSM1521754
30 GSM1521759.sga MRG|WCE|rep2 WCE GSM1521759
31 GSM1521730.sga NE|H3K27ac|rep1 H3K27ac GSM1521730
32 GSM1521735.sga NE|H3K27ac|rep2 H3K27ac GSM1521735
33 GSM1521731.sga NE|H3K27me3|rep1 H3K27me3 GSM1521731
34 GSM1521736.sga NE|H3K27me3|rep2 H3K27me3 GSM1521736
35 GSM1521732.sga NE|H3K4me1|rep1 H3K4me1 GSM1521732
36 GSM1521737.sga NE|H3K4me1|rep2 H3K4me1 GSM1521737
37 GSM1521733.sga NE|H3K4me3|rep1 H3K4me3 GSM1521733
38 GSM1521738.sga NE|H3K4me3|rep2 H3K4me3 GSM1521738
39 GSM1521760.sga NE|OTX2|rep1 OTX2 GSM1521760
40 GSM1521734.sga NE|WCE|rep1 WCE GSM1521734
41 GSM1521739.sga NE|WCE|rep2 WCE GSM1521739

Notes on samples nomenclature:

Cell types:

Sample types:

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).

References

Last update: 30 Mar 2016